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Nijveldt JJ, Rajan KK, Boersma K, Noorda EM, van der Starre-Gaal J, Kate MV'VT, Roeloffzen EMA, Vendel BN, Beek MA, Francken AB. Implementation of the Targeted Axillary Dissection Procedure in Clinically Node-Positive Breast Cancer: A Retrospective Analysis. Ann Surg Oncol 2024:10.1245/s10434-024-15182-3. [PMID: 38523225 DOI: 10.1245/s10434-024-15182-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/03/2024] [Indexed: 03/26/2024]
Abstract
BACKGROUND The targeted axillary dissection (TAD) procedure is used in clinically positive lymph node (cN+) breast cancer to assess whether pathological complete response (pCR) is achieved after neoadjuvant systemic therapy (NST) to decide on de-escalation of axillary lymph node dissection (ALND). In this study, we review the implementation of the TAD procedure in a large regional breast cancer center. METHODS All TAD procedures between 2016 and 2022 were reviewed. The TAD procedure consists of marking pre-NST the largest suspected metastatic lymph node(s) using a radioactive I-125 seed. During surgery, the marked node was excised together with a sentinel node procedure. Axillary therapy (ALND, axillary radiotherapy, or nothing) recommendations were based on the amount of suspected positive axillary lymph nodes (ALNs < 4 or ≥ 4) pre-NST and if pCR was achieved after NST. RESULTS A total of 312 TAD procedures were successfully performed in 309 patients. In 134 (43%) cases, pCR of the TAD lymph nodes were achieved. Per treatment protocol, 43 cases (14%) did not receive any axillary treatment, 218 cases (70%) received adjuvant axillary radiotherapy, and 51 cases (16%) underwent an ALND. During a median follow-up of 2.8 years, 46 patients (14%) developed recurrence, of which 11 patients (3.5%) had axillary recurrence. CONCLUSIONS Introduction of the TAD procedure has resulted in a reduction of 84% of previously indicated ALNDs. Moreover, 18% of cases did not receive adjuvant axillary radiotherapy. These data show that implementation of de-escalation axillary treatment with the TAD procedure appeared to be successful.
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Affiliation(s)
- Joni J Nijveldt
- Department of Surgical Oncology, Isala Zwolle, Zwolle, The Netherlands
| | - Kiran K Rajan
- Department of Surgical Oncology, Isala Zwolle, Zwolle, The Netherlands.
| | - Karina Boersma
- Department of Surgical Oncology, Isala Zwolle, Zwolle, The Netherlands
| | - Eva M Noorda
- Department of Surgical Oncology, Isala Zwolle, Zwolle, The Netherlands
| | | | | | | | - Brian N Vendel
- Department of Nuclear Medicine, Isala Zwolle, Zwolle, The Netherlands
| | - Maarten A Beek
- Department of Surgical Oncology, Isala Zwolle, Zwolle, The Netherlands
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Ortolani A, Lana D, Martucci A, Pesce F, Stallone S, Milani L, Urso R, Melucci G, Tigani D. Correlation between cephalic screw positioning of Standard Gamma 3 Nail for intertrochanteric fractures and cut-out incidence. SICOT J 2024; 10:9. [PMID: 38415767 PMCID: PMC10901073 DOI: 10.1051/sicotj/2024006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/27/2024] [Indexed: 02/29/2024] Open
Abstract
INTRODUCTION Lateral fractures of proximal femur are the most frequent fractures in elderly people. Internal fixation using medullary nails is the gold standard of treatment (Gamma 3 nail is the most implanted device) due to reduced incidence of complications than other devices. We report our experience in treating this kind of fractures with Gamma 3 nail, between January 2015 and December 2021. METHODS We performed a retrospective cohort study of patients treated in our orthopaedic department; level of clinical care is III: 559 patients (431 females and 128 males, with an average age of 85.3 years) with lateral femoral neck fracture. All patients were surgically treated with Gamma 3 standard nail (SGN). We evaluated preliminary X-rays to classify fractures, according to AO-OTA classification and post-operative X-ray to verify cephalic screw position site, according to areas described by Cleveland in 1959: we measured tip-to-apex distance (TAD) and tip-to-apex calcar referred distance (CalTAD). Finally Chang reduction quality criteria (CRQC) for fracture reduction of trochanteric fractures were determined using preoperative or postoperative Antero-Posterior (AP) and lateral radiographs in a Picture Archiving and Communication System (PACS). Incidence of cut-out was evaluated in relation with these parameters. Patients were divided into 2 groups: first group had cephalic screw in optimal positions (5-8-9), the other group had cephalic screw in other positions. RESULTS In 328 patients (58.7%) screw was in positions 5-8-9, in 231 patients (41.2%) screw was in not-optimal position. Median TAD was 19.1 ± 7.0 mm (range = 0.0-50.5); in 463 patients (82.8%) TAD was ≤ 25 mm. Median CalTAD was 21.4 ± 4.7 mm (range = 5.7-39.2); in 105 patients (79.4%) CalTAD was ≤ 25 mm. Cut-out was observed in 8 cases (1.43%). Multivariate analysis showed a significant correlation (p < 0,05) between incidence of cut-out and fracture type 31A2 and with TAD values >25 mm. Cephalic screw position did not influence incidence of cut-out. DISCUSSION In order to obtain fracture healing with a low risk of failure, in particular cut-out, it is necessary to obtain good reduction of fracture and optimal lag screw position in order to achieve a TAD inferior to 25 mm.
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Affiliation(s)
- Alessandro Ortolani
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
| | - Debora Lana
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
| | - Antonio Martucci
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
| | - Francesco Pesce
- Division of Renal Medicine, "Ospedale Isola Tiberina - Gemelli Isola", Via di Ponte Quattro capi, 39, 00186 Rome, Italy
| | - Stefano Stallone
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
| | - Lorenzo Milani
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
| | - Roberto Urso
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
| | - Giuseppe Melucci
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
| | - Domenico Tigani
- Department of Trauma and Orthopaedic Surgery, Maggiore Hospital, Largo Nigrisoli 2, 40133 Bologna, Italy
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Nakamura T, Ueda J, Mizuno S, Honda K, Kazuno AA, Yamamoto H, Hara T, Takata A. Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk. Cell Genom 2024; 4:100488. [PMID: 38280381 PMCID: PMC10879036 DOI: 10.1016/j.xgen.2024.100488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/24/2023] [Accepted: 01/02/2024] [Indexed: 01/29/2024]
Abstract
Whole-genome sequencing (WGS) studies of autism spectrum disorder (ASD) have demonstrated the roles of rare promoter de novo variants (DNVs). However, most promoter DNVs in ASD are not located immediately upstream of known ASD genes. In this study analyzing WGS data of 5,044 ASD probands, 4,095 unaffected siblings, and their parents, we show that promoter DNVs within topologically associating domains (TADs) containing ASD genes are significantly and specifically associated with ASD. An analysis considering TADs as functional units identified specific TADs enriched for promoter DNVs in ASD and indicated that common variants in these regions also confer ASD heritability. Experimental validation using human induced pluripotent stem cells (iPSCs) showed that likely deleterious promoter DNVs in ASD can influence multiple genes within the same TAD, resulting in overall dysregulation of ASD-associated genes. These results highlight the importance of TADs and gene-regulatory mechanisms in better understanding the genetic architecture of ASD.
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Affiliation(s)
- Takumi Nakamura
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Junko Ueda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan.
| | - Shota Mizuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kurara Honda
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - An-A Kazuno
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hirona Yamamoto
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Tomonori Hara
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Department of Organ Anatomy, Tohoku University Graduate School of Medicine, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan; Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo 113-8421, Japan.
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Zhang M, Huang H, Li J, Wu Q. ZNF143 deletion alters enhancer/promoter looping and CTCF/cohesin geometry. Cell Rep 2024; 43:113663. [PMID: 38206813 DOI: 10.1016/j.celrep.2023.113663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/28/2023] [Accepted: 12/22/2023] [Indexed: 01/13/2024] Open
Abstract
The transcription factor ZNF143 contains a central domain of seven zinc fingers in a tandem array and is involved in 3D genome construction. However, the mechanism by which ZNF143 functions in chromatin looping remains unclear. Here, we show that ZNF143 directionally recognizes a diverse range of genomic sites directly within enhancers and promoters and is required for chromatin looping between these sites. In addition, ZNF143 is located between CTCF and cohesin at numerous CTCF sites, and ZNF143 removal narrows the space between CTCF and cohesin. Moreover, genetic deletion of ZNF143, in conjunction with acute CTCF degradation, reveals that ZNF143 and CTCF collaborate to regulate higher-order topological chromatin organization. Finally, CTCF depletion enlarges direct ZNF143 chromatin looping. Thus, ZNF143 is recruited by CTCF to the CTCF sites to regulate CTCF/cohesin configuration and TAD (topologically associating domain) formation, whereas directional recognition of genomic DNA motifs directly by ZNF143 itself regulates promoter activity via chromatin looping.
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Affiliation(s)
- Mo Zhang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Haiyan Huang
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Jingwei Li
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China
| | - Qiang Wu
- Center for Comparative Biomedicine, Ministry of Education Key Laboratory of Systems Biomedicine, State Key Laboratory of Medical Genomics, Institute of Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; WLA Laboratories, Shanghai 201203, China.
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Shevelyov YY. Interactions of Chromatin with the Nuclear Lamina and Nuclear Pore Complexes. Int J Mol Sci 2023; 24:15771. [PMID: 37958755 PMCID: PMC10649103 DOI: 10.3390/ijms242115771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/26/2023] [Accepted: 10/29/2023] [Indexed: 11/15/2023] Open
Abstract
Heterochromatin and euchromatin form different spatial compartments in the interphase nucleus, with heterochromatin being localized mainly at the nuclear periphery. The mechanisms responsible for peripheral localization of heterochromatin are still not fully understood. The nuclear lamina and nuclear pore complexes were obvious candidates for the role of heterochromatin binders. This review is focused on recent studies showing that heterochromatin interactions with the nuclear lamina and nuclear pore complexes maintain its peripheral localization. Differences in chromatin interactions with the nuclear envelope in cell populations and in individual cells are also discussed.
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Affiliation(s)
- Yuri Y Shevelyov
- Laboratory of Analysis of Gene Regulation, National Research Centre "Kurchatov Institute", Kurchatov Sq. 2, 123182 Moscow, Russia
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Umeh OD, Offojebe UL, Isiekwe IG, Utomi I, daCosta O. Survival analysis of temporary anchorage devices: A retrospective analysis in a Nigerian orthodontic patient population. J Orthod Sci 2023; 12:45. [PMID: 37881656 PMCID: PMC10597358 DOI: 10.4103/jos.jos_10_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/19/2023] [Accepted: 04/14/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVES Temporary anchorage devices (TADs) are skeletal anchorage devices. They are minimally invasive and placed by the orthodontist to prevent unwanted tooth movement. This study evaluated the survival rate of orthodontic TADs at 6 months. This study also assessed the effect of age, gender, side, site, dental arch of placement, and length of the TADs on its survival rate. MATERIALS AND METHODS Ethical approval was obtained from the Health Research Ethics Committee of the hospital. The study sample comprised orthodontic patients who required the placement of TADs during treatment at a private dental facility in Lagos. Data for the study were obtained from the case files of the study subjects and included the subjects' age, gender, date of placement of the TADs, the site, side and arch of placement, the length of the TADs, and the survival rate of 6 months after placement. RESULTS We reviewed 90 placed TADs and observed a survival rate of 88.9%. Most TAD failures occurred in the first month of placement (p = 001). There was no observable statistically significant effect of all other variables assessed (age, gender, arch, site, side, or implant length) on the survival rate of the TADs. CONCLUSIONS The survival rate of TADs was high. Most TAD failures significantly occurred within one month of placement. There was no significant association between all other clinical variables and orthodontic mini-implant survival.
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Affiliation(s)
- Onyinye Dorothy Umeh
- Department of Child Dental Health, Faculty of Dental Sciences, Lagos University Teaching Hospital, Idi-Araba, Lagos, Nigeria
| | - Uzoma Linda Offojebe
- Department of Child Dental Health, Faculty of Dental Sciences, College of Medicine, University of Lagos, Idi-Araba/Lagos University Teaching Hospital, Idi-Araba, Lagos, Nigeria
| | - Ikenna Gerald Isiekwe
- Department of Child Dental Health, Faculty of Dental Sciences, College of Medicine, University of Lagos, Idi-Araba/Lagos University Teaching Hospital, Idi-Araba, Lagos, Nigeria
| | - Ifeoma Utomi
- Department of Child Dental Health, Faculty of Dental Sciences, College of Medicine, University of Lagos, Idi-Araba/Lagos University Teaching Hospital, Idi-Araba, Lagos, Nigeria
| | - Oluranti daCosta
- Department of Child Dental Health, Faculty of Dental Sciences, College of Medicine, University of Lagos, Idi-Araba/Lagos University Teaching Hospital, Idi-Araba, Lagos, Nigeria
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Mohana G, Dorier J, Li X, Mouginot M, Smith RC, Malek H, Leleu M, Rodriguez D, Khadka J, Rosa P, Cousin P, Iseli C, Restrepo S, Guex N, McCabe BD, Jankowski A, Levine MS, Gambetta MC. Chromosome-level organization of the regulatory genome in the Drosophila nervous system. Cell 2023; 186:3826-3844.e26. [PMID: 37536338 PMCID: PMC10529364 DOI: 10.1016/j.cell.2023.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/31/2023] [Accepted: 07/06/2023] [Indexed: 08/05/2023]
Abstract
Previous studies have identified topologically associating domains (TADs) as basic units of genome organization. We present evidence of a previously unreported level of genome folding, where distant TAD pairs, megabases apart, interact to form meta-domains. Within meta-domains, gene promoters and structural intergenic elements present in distant TADs are specifically paired. The associated genes encode neuronal determinants, including those engaged in axonal guidance and adhesion. These long-range associations occur in a large fraction of neurons but support transcription in only a subset of neurons. Meta-domains are formed by diverse transcription factors that are able to pair over long and flexible distances. We present evidence that two such factors, GAF and CTCF, play direct roles in this process. The relative simplicity of higher-order meta-domain interactions in Drosophila, compared with those previously described in mammals, allowed the demonstration that genomes can fold into highly specialized cell-type-specific scaffolds that enable megabase-scale regulatory associations.
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Affiliation(s)
- Giriram Mohana
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Julien Dorier
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Xiao Li
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Marion Mouginot
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Rebecca C Smith
- Brain Mind Institute, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Héléna Malek
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Marion Leleu
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Daniel Rodriguez
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jenisha Khadka
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Patrycja Rosa
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland
| | - Pascal Cousin
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Christian Iseli
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Simon Restrepo
- Arcoris bio AG, Lüssirainstrasse 52, 6300 Zug, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, 1015 Lausanne, Switzerland; Bioinformatics Competence Center, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Brian D McCabe
- Brain Mind Institute, Swiss Federal Institute of Technology Lausanne, 1015 Lausanne, Switzerland
| | - Aleksander Jankowski
- Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland.
| | - Michael S Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
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Li A, Zeng G, Wang H, Li X, Zhang Z. DeDoc2 Identifies and Characterizes the Hierarchy and Dynamics of Chromatin TAD-Like Domains in the Single Cells. Adv Sci (Weinh) 2023:e2300366. [PMID: 37162225 PMCID: PMC10369259 DOI: 10.1002/advs.202300366] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/18/2023] [Indexed: 05/11/2023]
Abstract
Topologically associating domains (TADs) are functional chromatin units with hierarchical structure. However, the existence, prevalence, and dynamics of such hierarchy in single cells remain unexplored. Here, a new generation TAD-like domain (TLD) detection algorithm, named deDoc2, to decode the hierarchy of TLDs in single cells, is reported. With dynamic programming, deDoc2 seeks genome partitions with global minimal structure entropy for both whole and local contact matrix. Notably, deDoc2 outperforms state-of-the-art tools and is one of only two tools able to identify the hierarchy of TLDs in single cells. By applying deDoc2, it is showed that the hierarchy of TLDs in single cells is highly dynamic during cell cycle, as well as among human brain cortex cells, and that it is associated with cellular identity and functions. Thus, the results demonstrate the abundance of information potentially encoded by TLD hierarchy for functional regulation. The deDoc2 can be freely accessed at https://github.com/zengguangjie/deDoc2.
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Affiliation(s)
- Angsheng Li
- State Key Laboratory of Software Development Environment, School of Computer Science, Beihang University, Beijing, 100191, P. R. China
- Zhongguancun Laboratory, Beijing, 100094, P. R. China
| | - Guangjie Zeng
- State Key Laboratory of Software Development Environment, School of Computer Science, Beihang University, Beijing, 100191, P. R. China
| | - Haoyu Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, 101408, P. R. China
| | - Xiao Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, 101408, P. R. China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing, 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, 101408, P. R. China
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Yashima Y, Kaku M, Yamamoto T, Medina CC, Ono S, Takeda Y, Tanimoto K. Camouflage Correction of Skeletal Class III Severe Open Bite with Tooth Ankylosis Treated by Temporary Anchorage Devices: A Case Report. Dent J (Basel) 2023; 11:dj11040107. [PMID: 37185485 PMCID: PMC10136872 DOI: 10.3390/dj11040107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/12/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
Tooth ankylosis is a disorder characterized by the fusion of tooth and alveolar bone. This case report describes the treatment of a severe open bite due to tooth ankylosis. A 14-year-old female patient with a chief complaint of masticatory dysfunction was diagnosed with skeletal Class III severe anterior open bite and tooth ankylosis. She visited our university hospital with a chief complaint of an anterior open bite. After the surgical luxation of the ankylosed maxillary right central incisor, the tooth was orthodontically retracted using a nickel-titanium wire. The right mandibular lateral incisor and canine were luxated and retracted using intermaxillary elastics from a temporary anchorage device (TAD), which was inserted in the opposite jaw. During the treatment, skeletal Class III malocclusion deteriorated due to anterior growth of the mandible. Therefore, TADs were inserted into the retromolar pad on both sides of the mandible and retracted into the mandibular dental arch. Although the mandibular right canine was luxated several times, it could not be brought to the occlusal line, and was thus extracted; the extraction space was replaced with a prosthesis. Consequently, a normal overjet and overbite with a straight profile were achieved. Extrusion of ankylosed teeth by intermaxillary elastics from a TAD is a valid treatment option for patients with severe open bites.
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Affiliation(s)
- Yuka Yashima
- Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Masato Kaku
- Department of Anatomy and Functional Restorations, Division of Oral Health Sciences, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Taeko Yamamoto
- Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Cynthia Concepcion Medina
- Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Shigehiro Ono
- Department of Oral and Maxillofacial Surgery, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
| | - Yosuke Takeda
- Dental Practitioner, Yumemirai Dental & Orthodontic Clinic Saijo, 1172 Sukezane, Saijo, Higashi Hiroshima 739-0021, Japan
| | - Kotaro Tanimoto
- Department of Orthodontics and Craniofacial Developmental Biology, Graduate School of Biomedical Sciences, Hiroshima University, 1-2-3 Kasumi, Minami-ku, Hiroshima 734-0037, Japan
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10
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Kim TW, Hwang SJ, Wu T. Treatment of anterior open bite and an ankylosed incisor by applying multiloop edgewise archwire, mini-implants, and dentoalveolar distraction. Angle Orthod 2023:491024. [PMID: 36856738 DOI: 10.2319/070122-472.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 12/01/2022] [Indexed: 03/02/2023] Open
Abstract
An 18.7-year-old female patient with an anterior open bite and an ankylosed left maxillary central incisor was referred from a private orthodontic clinic. Canine relationships were Class II and molar relationships were Class I. The open bite was closed with the multiloop edgewise archwire and up-and-down elastics. The maxillary left central incisor was extruded by dentoalveolar distraction assisted with mini-implants. Active treatment took 2 years and 1 month, and the treatment result remained stable 14 months after debonding.
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11
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Rheinberger M, Costa AL, Kampmann M, Glavas D, Shytaj IL, Sreeram S, Penzo C, Tibroni N, Garcia-Mesa Y, Leskov K, Fackler OT, Vlahovicek K, Karn J, Lucic B, Herrmann C, Lusic M. Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains. Cell Rep 2023; 42:112110. [PMID: 36790927 DOI: 10.1016/j.celrep.2023.112110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 02/16/2023] Open
Abstract
HIV-1 encounters the hierarchically organized host chromatin to stably integrate and persist in anatomically distinct latent reservoirs. The contribution of genome organization in HIV-1 infection has been largely understudied across different HIV-1 targets. Here, we determine HIV-1 integration sites (ISs), associate them with chromatin and expression signatures at different genomic scales in a microglia cell model, and profile them together with the primary T cell reservoir. HIV-1 insertions into introns of actively transcribed genes with IS hotspots in genic and super-enhancers, characteristic of blood cells, are maintained in the microglia cell model. Genome organization analysis reveals dynamic CCCTC-binding factor (CTCF) clusters in cells with active and repressed HIV-1 transcription, whereas CTCF removal impairs viral integration. We identify CTCF-enriched topologically associated domain (TAD) boundaries with signatures of transcriptionally active chromatin as HIV-1 integration determinants in microglia and CD4+ T cells, highlighting the importance of host genome organization in HIV-1 infection.
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Affiliation(s)
- Mona Rheinberger
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Ana Luisa Costa
- Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, 69120 Heidelberg, Germany
| | - Martin Kampmann
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Dunja Glavas
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Iart Luca Shytaj
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Sheetal Sreeram
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Carlotta Penzo
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Nadine Tibroni
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Yoelvis Garcia-Mesa
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Konstantin Leskov
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Oliver T Fackler
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany
| | - Kristian Vlahovicek
- Bioinformatics Group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Bojana Lucic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany.
| | - Carl Herrmann
- Health Data Science Unit, Medical Faculty University Heidelberg and BioQuant, 69120 Heidelberg, Germany.
| | - Marina Lusic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital, 69120 Heidelberg, Germany; German Center for Infection Research (DZIF), 69120 Heidelberg, Germany.
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12
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Abstract
A key maxim in modernist architecture is that 'form follows function'. While modernist buildings are hopefully the product of intelligent design, the architectures of chromosomes have been sculpted by the forces of evolution over many thousands of generations. In the following, I will describe recent advances in our understanding of chromosome architecture in the archaeal domain of life. Although much remains to be learned about the mechanistic details of archaeal chromosome organization, some general principles have emerged. At the 10-100 kb level, archaeal chromosomes have a conserved local organization reminiscent of bacterial genomes. In contrast, lineage-specific innovations appear to have imposed distinct large-scale architectural features. The ultimate functions of genomes are to store and to express genetic information. Gene expression profiles have been shown to influence chromosome architecture, thus their form follows function. However, local changes to chromosome conformation can also influence gene expression and therefore, in these instances, function follows form.
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Affiliation(s)
- Stephen D. Bell
- Molecular and Cellular Biochemistry Department, Indiana University, Bloomington, IN 47405, U.S.A
- Biology Department, Indiana University, Bloomington, IN 47405, U.S.A
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13
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Preger-Ben Noon E, Frankel N. Can changes in 3D genome architecture create new regulatory landscapes that contribute to phenotypic evolution? Essays Biochem 2022; 66:745-52. [PMID: 36250960 DOI: 10.1042/EBC20220057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 12/13/2022]
Abstract
Animal genomes are compartmentalized into insulated regulatory units named topology-associated domains (TADs). TADs insulate gene promoters from enhancers that occupy neighboring TADs. Chromosomal rearrangements that disrupt TAD structure can generate new regulatory interactions between enhancers and promoters that were once separated into different TADs, which might lead to new gene expression patterns. On the one hand, TAD rearrangements are known to cause deleterious phenotypes, but, on the other hand, rearrangements can also create novel expression patterns that may be selected during evolution because they generate advantageous phenotypes. Here, we review recent studies that explore the effects of chromosomal rearrangements and genetic perturbations on TAD structure and gene regulation in the context of development and evolution. We discuss the possible contribution of evolutionary breakpoints (EBRs) that affect TAD structure to the evolution of gene regulation and the phenotype.
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14
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Yang JY, Chang JM. Pattern recognition of topologically associating domains using deep learning. BMC Bioinformatics 2022; 22:634. [PMID: 36482308 PMCID: PMC9732975 DOI: 10.1186/s12859-022-05075-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/22/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Recent increasing evidence indicates that three-dimensional chromosome structure plays an important role in genomic function. Topologically associating domains (TADs) are self-interacting regions that have been shown to be a chromosomal structural unit. During evolution, these are conserved based on checking synteny block cross species. Are there common TAD patterns across species or cell lines? RESULTS To address the above question, we propose a novel task-TAD recognition-as opposed to traditional TAD identification. Specifically, we treat Hi-C maps as images, thus re-casting TAD recognition as image pattern recognition, for which we use a convolutional neural network and a residual neural network. In addition, we propose an elegant way to generate non-TAD data for binary classification. We demonstrate deep learning performance which is quite promising, AUC > 0.80, through cross-species and cell-type validation. CONCLUSIONS TADs have been shown to be conserved during evolution. Interestingly, our results confirm that the TAD recognition model is practical across species, which indicates that TADs between human and mouse show common patterns from an image classification point of view. Our approach could be a new way to identify TAD variations or patterns among Hi-C maps. For example, TADs of two Hi-C maps are conserved if the two classification models are exchangeable.
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Affiliation(s)
- Jhen Yuan Yang
- grid.412042.10000 0001 2106 6277Department of Computer Science, National Chengchi University, 11605 Taipei City, Taiwan
| | - Jia-Ming Chang
- grid.412042.10000 0001 2106 6277Department of Computer Science, National Chengchi University, 11605 Taipei City, Taiwan
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15
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Kyriakopoulos G, Panagopoulos A, Pasiou E, Kourkoulis SK, Diamantakos I, Anastopoulos G, Tserpes K, Tatani I, Lakoumentas J, Megas P. Optimizing fixation methods for stable and unstable intertrochanteric hip fractures treated with sliding hip screw or cephalomedullary nailing: A comparative biomechanical and finite element analysis study. Injury 2022; 53:4072-4085. [PMID: 36272844 DOI: 10.1016/j.injury.2022.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 09/19/2022] [Accepted: 10/05/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND Despite recent advances in implants and surgical techniques, catastrophic and clinical failures in the treatment of intertrochanteric fractures continue to occur, with dire consequences in an overall frail population subset. The aim of the current study is to evaluate the effect of the factors under the surgeons' control, namely fracture reduction and implant selection, on the biomechanical behavior of fracture fixation constructs. MATERIAL-METHODS An experimental protocol was conducted with the use of instrumented sawbones, in order to validate the finite element models. The implants used were the Gamma3®and DHS systems. Subsequently, a series of scenaria were considered, including various reduction and implant angle combinations. Data were retrieved concerning the peak cancellous bone stresses around the hip screw and the volume of cancellous bone in the femoral head stressed at critical levels, as well as implant stresses and stresses on the cortical bone of the distal fragment. RESULTS All stable fracture models displayed significantly decreased cancellous bone stresses and implant stresses compared to their unstable counterparts, regardless of implant used. The effect of increasing implant angle led to a decrease in implant stresses in all models studied, but had a beneficial effect on the stresses in the cancellous bone of the proximal fragment only in the subgroups of stable fractures with both implants and unstable fractures treated with a cephalomedullary nail (CMN). In unstable fractures anatomically reduced, the use of CMN led to significantly lower peak stresses in the cancellous bone and a smaller volume of bone stressed at critical levels. Increasing the reduction angle by 5 ° led to a significant decrease in both peak stresses and volume of bone stressed at critical levels, more prominent in the sliding hip screw (SHS) models. Decreasing the reduction angle into varus by 5 or 10 ° led to a significant increase in bone and implant stresses regardless of implant used. CONCLUSIONS In stable two-part (AO31.A2) fractures the use of the SHS appears to be biomechanically equivalent to CMN. In unstable, anatomically reduced fractures, the use of CMN leads to significantly reduced cancellous bone stresses and decreased rotation of the proximal fragment during loading. A reduction in varus should be avoided at all costs. In unstable fractures treated with SHS a reduction in slight valgus appears to be biomechanically beneficial. The highest implant angle that allows for proper screw position and trajectory in the femoral head should be used for stable fractures with both implants and unstable fractures treated with Gamma3®.
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Affiliation(s)
- G Kyriakopoulos
- Department of Orthopaedics, "Georgios Gennimatas" General Hospital, Athens, Greece.
| | - A Panagopoulos
- Department of Adult Reconstruction, Orthopaedic Clinic, Patras University Hospital, Patras, Greece
| | - E Pasiou
- Laboratory of Biomechanics and Biomedical Physics, Department of Mechanics, School of Applied Mathematical and Physical Sciences, NTUA, Greece
| | - S K Kourkoulis
- Laboratory of Biomechanics and Biomedical Physics, Department of Mechanics, School of Applied Mathematical and Physical Sciences, NTUA, Greece
| | - I Diamantakos
- Department of Mechanical Engineering, School of Engineering, University of the Peloponnese, Patras, Greece
| | - G Anastopoulos
- Department of Orthopaedics, "Georgios Gennimatas" General Hospital, Athens, Greece
| | - K Tserpes
- Laboratory of Technology and Strength of Materials, Department of Mechanical Engineering and Aeronautics, University of Patras, Patras, Greece
| | - I Tatani
- Department of Adult Reconstruction, Orthopaedic Clinic, Patras University Hospital, Patras, Greece
| | - J Lakoumentas
- Department of Medical Physics, School of Medicine, University of Patras, Greece
| | - P Megas
- Department of Adult Reconstruction, Orthopaedic Clinic, Patras University Hospital, Patras, Greece
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16
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Rossini R, Kumar V, Mathelier A, Rognes T, Paulsen J. MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biol 2022; 23:247. [PMID: 36451166 PMCID: PMC9710047 DOI: 10.1186/s13059-022-02815-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
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Affiliation(s)
- Roberto Rossini
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Vipin Kumar
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Anthony Mathelier
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Torbjørn Rognes
- grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Jonas Paulsen
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
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17
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Mohajeri K, Yadav R, D'haene E, Boone PM, Erdin S, Gao D, Moyses-Oliveira M, Bhavsar R, Currall BB, O'Keefe K, Burt ND, Lowther C, Lucente D, Salani M, Larson M, Redin C, Dudchenko O, Aiden EL, Menten B, Tai DJC, Gusella JF, Vergult S, Talkowski ME. Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models. Am J Hum Genet 2022; 109:2049-2067. [PMID: 36283406 PMCID: PMC9674968 DOI: 10.1016/j.ajhg.2022.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/29/2022] [Indexed: 01/26/2023] Open
Abstract
Point mutations and structural variants that directly disrupt the coding sequence of MEF2C have been associated with a spectrum of neurodevelopmental disorders (NDDs). However, the impact of MEF2C haploinsufficiency on neurodevelopmental pathways and synaptic processes is not well understood, nor are the complex mechanisms that govern its regulation. To explore the functional changes associated with structural variants that alter MEF2C expression and/or regulation, we generated an allelic series of 204 isogenic human induced pluripotent stem cell (hiPSC)-derived neural stem cells and glutamatergic induced neurons. These neuronal models harbored CRISPR-engineered mutations that involved direct deletion of MEF2C or deletion of the boundary points for topologically associating domains (TADs) and chromatin loops encompassing MEF2C. Systematic profiling of mutation-specific alterations, contrasted to unedited controls that were exposed to the same guide RNAs for each edit, revealed that deletion of MEF2C caused differential expression of genes associated with neurodevelopmental pathways and synaptic function. We also discovered significant reduction in synaptic activity measured by multielectrode arrays (MEAs) in neuronal cells. By contrast, we observed robust buffering against MEF2C regulatory disruption following deletion of a distal 5q14.3 TAD and loop boundary, whereas homozygous loss of a proximal loop boundary resulted in down-regulation of MEF2C expression and reduced electrophysiological activity on MEA that was comparable to direct gene disruption. Collectively, these studies highlight the considerable functional impact of MEF2C deletion in neuronal cells and systematically characterize the complex interactions that challenge a priori predictions of regulatory consequences from structural variants that disrupt three-dimensional genome organization.
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Affiliation(s)
- Kiana Mohajeri
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Rachita Yadav
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Eva D'haene
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Philip M Boone
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Serkan Erdin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Dadi Gao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Mariana Moyses-Oliveira
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Riya Bhavsar
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin B Currall
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kathryn O'Keefe
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nicholas D Burt
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Chelsea Lowther
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Diane Lucente
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Monica Salani
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mathew Larson
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Claire Redin
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX, USA; UWA School of Agriculture and Environment, The University of Western Australia, Crawley, WA 6009, Australia; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech, Pudong, China
| | - Björn Menten
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Derek J C Tai
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - James F Gusella
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA; Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Sarah Vergult
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA; Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA.
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18
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Gong H, Yang Y, Zhang X, Li M, Zhang S, Chen Y. CASPIAN: A method to identify chromatin topological associated domains based on spatial density cluster. Comput Struct Biotechnol J 2022; 20:4816-4824. [PMID: 36147659 PMCID: PMC9464881 DOI: 10.1016/j.csbj.2022.08.059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 08/10/2022] [Accepted: 08/27/2022] [Indexed: 11/25/2022] Open
Abstract
With the development of Hi-C technology, the detection of topologically associated domains (TADs) boundaries plays an important role in exploring the relationship between gene structure and expression. However, a method that can identify accurate TAD boundaries from the Hi-C contact matrix with different resolutions is currently lacking. We proposed a method named CASPIAN that can identify chromatin TAD boundaries based on the spatial density clustering algorithm. CASPIAN requires few parameters to call TADs. This method is realized using the hierarchical density-based clustering method HDBSCAN, where the distance of pairwise bins is calculated based on three distance metrics (Euclidean, Manhattan, and Chebyshev distance metric) to adapt to the characteristics of the Hi-C contact matrix generated from simulation experiments or normalized methods. Our results show that, same as standard methods (e.g., Insulation Score, TopDom), CASPIAN can enrich factors related to promoting the gene expression, such as CTCF, H3K4me1, H3K4me3, RAD21, POLR2A, and SMC3. We also calculated the approximate proportion of various factors anchored at the TAD boundaries to observe the distribution of these factors surrounding the TAD boundaries. In conclusion, CASPIAN is an easy method to explore the relationship between transcription factors and TAD boundaries. CASPIAN is available online (https://gitee.com/ghaiyan/caspian).
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Affiliation(s)
- Haiyan Gong
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yi Yang
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Xiaotong Zhang
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China.,Shunde Graduate School, University of Science and Technology Beijing, Foshan 528399, Guangdong, China
| | - Minghong Li
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Sichen Zhang
- School of Computer and Communication Engineering, Beijing Key Laboratory of Knowledge Engineering for Materials Science, Beijing Advanced Innovation Center for Materials Genome Engineering, University of Science and Technology Beijing, Beijing 100083, China
| | - Yang Chen
- The State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China
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19
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Lebeau B, Jangal M, Zhao T, Wong CK, Wong N, Cañedo EC, Hébert S, Aguilar-Mahecha A, Chabot C, Buchanan M, Catterall R, McCaffrey L, Deblois G, Kleinman C, Park M, Basik M, Witcher M. 3D chromatin remodeling potentiates transcriptional programs driving cell invasion. Proc Natl Acad Sci U S A 2022; 119:e2203452119. [PMID: 36037342 DOI: 10.1073/pnas.2203452119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The contribution of deregulated chromatin architecture, including topologically associated domains (TADs), to cancer progression remains ambiguous. CCCTC-binding factor (CTCF) is a central regulator of higher-order chromatin structure that undergoes copy number loss in over half of all breast cancers, but the impact of this defect on epigenetic programming and chromatin architecture remains unclear. We find that under physiological conditions, CTCF organizes subTADs to limit the expression of oncogenic pathways, including phosphatidylinositol 3-kinase (PI3K) and cell adhesion networks. Loss of a single CTCF allele potentiates cell invasion through compromised chromatin insulation and a reorganization of chromatin architecture and histone programming that facilitates de novo promoter-enhancer contacts. However, this change in the higher-order chromatin landscape leads to a vulnerability to inhibitors of mTOR. These data support a model whereby subTAD reorganization drives both modification of histones at de novo enhancer-promoter contacts and transcriptional up-regulation of oncogenic transcriptional networks.
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20
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Sun Z, Wang Y, Song Z, Zhang H, Wang Y, Liu K, Ma M, Wang P, Fang Y, Cai D, Li G, Fang Y. DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication. J Adv Res 2022; 42:41-53. [PMID: 35933090 DOI: 10.1016/j.jare.2022.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 07/05/2022] [Accepted: 07/23/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Polyploidy is a major force in plant evolution and the domestication of cultivated crops. OBJECTIVES The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication. METHODS The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication. RESULTS We found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes. CONCLUSION The study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.
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Abstract
Meiosis increases genetic diversity in offspring by generating genetically unique haploid gametes with reshuffled chromosomes. This process requires a specialized set of meiotic proteins, which facilitate chromosome recombination and segregation. However, re-expression of meiotic proteins in mitosis can have catastrophic oncogenic consequences and aberrant expression of meiotic proteins is a common occurrence in human tumors. Mechanistically, re-activation of meiotic genes in cancer promotes oncogenesis likely because cancers-conversely to healthy mitosis-are fueled by genetic instability which promotes tumor evolution, and evasion of immune response and treatment pressure. In this review, we explore similarities between meiotic and cancer cells with a particular focus on the oncogenic activation of meiotic genes in cancer. We emphasize the role of histones and their modifications, DNA methylation, genome organization, R-loops and the availability of distal enhancers.
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Campbell M, Chantarasrivong C, Yanagihashi Y, Inagaki T, Davis RR, Nakano K, Kumar A, Tepper CG, Izumiya Y. KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin. J Virol 2022; 96:e0056522. [PMID: 35867573 DOI: 10.1128/jvi.00565-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 bp resolution and constructed a 3D KSHV genomic structural model with 2 kb binning. The latent KSHV genome formed very similar genomic architectures in three different naturally infected PEL cell lines and in an experimentally infected epithelial cell line. The majority of the TAD boundaries were occupied by structural maintenance of chromosomes (SMC1) cohesin complex and CCCTC-binding factor (CTCF), and the KSHV transactivator was recruited to those sites during reactivation. Triggering KSHV gene expression decreased prewired genomic loops within the regulatory unit, while contacts extending outside of regulatory borders increased, leading to formation of a larger regulatory unit with a shift from repressive to active compartments (B to A). The 3D genomic structural model proposes that the immediate early promoter region is localized on the periphery of the 3D viral genome during latency, while highly inducible noncoding RNA regions moved toward the inner space of the structure, resembling the configuration of a "bird cage" during reactivation. The compartment-like properties of viral episomal chromatin structure and its reorganization during the transition from latency may help facilitate viral gene transcription. IMPORTANCE The 3D architecture of chromatin allows for efficient arrangement, expression, and replication of genetic material. The genomes of all organisms studied to date have been found to be organized through some form of tiered domain structures. However, the architectural framework of the genomes of large double-stranded DNA viruses such as the herpesvirus family has not been reported. Prior studies with Kaposi's sarcoma-associated herpesvirus (KSHV) have indicated that the viral chromatin shares many biological properties exhibited by the host cell genome, essentially behaving as a mini human chromosome. Thus, we hypothesized that the KSHV genome may be organized in a similar manner. In this report, we describe the domain structure of the latent and lytic KSHV genome at 500 bp resolution and present a 3D genomic structural model for KSHV under each condition. These results add new insights into the complex regulation of the viral life cycle.
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Taylor T, Sikorska N, Shchuka VM, Chahar S, Ji C, Macpherson NN, Moorthy SD, de Kort MAC, Mullany S, Khader N, Gillespie ZE, Langroudi L, Tobias IC, Lenstra TL, Mitchell JA, Sexton T. Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus. Genes Dev 2022; 36:699-717. [PMID: 35710138 PMCID: PMC9296009 DOI: 10.1101/gad.349489.122] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 06/03/2022] [Indexed: 11/24/2022]
Abstract
How distal regulatory elements control gene transcription and chromatin topology is not clearly defined, yet these processes are closely linked in lineage specification during development. Through allele-specific genome editing and chromatin interaction analyses of the Sox2 locus in mouse embryonic stem cells, we found a striking disconnection between transcriptional control and chromatin architecture. We traced nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletions have no effect on promoter-enhancer interaction frequencies or topological domain organization. Local chromatin architecture maintenance, including at the topologically associating domain (TAD) boundary downstream from the Sox2 enhancer, is widely distributed over multiple transcription factor-bound regions and maintained in a CTCF-independent manner. Furthermore, partial disruption of promoter-enhancer interactions by ectopic chromatin loop formation has no effect on Sox2 transcription. These findings indicate that many transcription factors are involved in modulating chromatin architecture independently of CTCF.
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Affiliation(s)
- Tiegh Taylor
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Natalia Sikorska
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Virlana M Shchuka
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Sanjay Chahar
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
| | - Chenfan Ji
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Neil N Macpherson
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Sakthi D Moorthy
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Marit A C de Kort
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Shanelle Mullany
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Nawrah Khader
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Zoe E Gillespie
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Lida Langroudi
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Ian C Tobias
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Tineke L Lenstra
- Division of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada
| | - Tom Sexton
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France
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Popay TM, Dixon JR. Coming full circle: on the origin and evolution of the looping model for enhancer-promoter communication. J Biol Chem 2022; 298:102117. [PMID: 35691341 PMCID: PMC9283939 DOI: 10.1016/j.jbc.2022.102117] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/05/2022] Open
Abstract
In mammalian organisms, enhancers can regulate transcription from great genomic distances. How enhancers affect distal gene expression has been a major question in the field of gene regulation. One model to explain how enhancers communicate with their target promoters, the chromatin looping model, posits that enhancers and promoters come in close spatial proximity to mediate communication. Chromatin looping has been broadly accepted as a means for enhancer–promoter communication, driven by accumulating in vitro and in vivo evidence. The genome is now known to be folded into a complex 3D arrangement, created and maintained in part by the interplay of the Cohesin complex and the DNA-binding protein CTCF. In the last few years, however, doubt over the relationship between looping and transcriptional activation has emerged, driven by studies finding that only a modest number of genes are perturbed with acute degradation of looping machinery components. In parallel, newer models describing distal enhancer action have also come to prominence. In this article, we explore the emergence and development of the looping model as a means for enhancer–promoter communication and review the contrasting evidence between historical gene-specific and current global data for the role of chromatin looping in transcriptional regulation. We also discuss evidence for alternative models to chromatin looping and their support in the literature. We suggest that, while there is abundant evidence for chromatin looping as a major mechanism for enhancer function, enhancer–promoter communication is likely mediated by more than one mechanism in an enhancer- and context-dependent manner.
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Affiliation(s)
- Tessa M Popay
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R Dixon
- Gene Expression Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
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Franke M, Daly AF, Palmeira L, Tirosh A, Stigliano A, Trifan E, Faucz FR, Abboud D, Petrossians P, Tena JJ, Vitali E, Lania AG, Gómez-Skarmeta JL, Beckers A, Stratakis CA, Trivellin G. Duplications disrupt chromatin architecture and rewire GPR101-enhancer communication in X-linked acrogigantism. Am J Hum Genet 2022; 109:553-570. [PMID: 35202564 DOI: 10.1016/j.ajhg.2022.02.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/01/2022] [Indexed: 02/04/2023] Open
Abstract
X-linked acrogigantism (X-LAG) is the most severe form of pituitary gigantism and is characterized by aggressive growth hormone (GH)-secreting pituitary tumors that occur in early childhood. X-LAG is associated with chromosome Xq26.3 duplications (the X-LAG locus typically includes VGLL1, CD40LG, ARHGEF6, RBMX, and GPR101) that lead to massive pituitary tumoral expression of GPR101, a novel regulator of GH secretion. The mechanism by which the duplications lead to marked pituitary misexpression of GPR101 alone was previously unclear. Using Hi-C and 4C-seq, we characterized the normal chromatin structure at the X-LAG locus. We showed that GPR101 is located within a topologically associating domain (TAD) delineated by a tissue-invariant border that separates it from centromeric genes and regulatory sequences. Next, using 4C-seq with GPR101, RBMX, and VGLL1 viewpoints, we showed that the duplications in multiple X-LAG-affected individuals led to ectopic interactions that crossed the invariant TAD border, indicating the existence of a similar and consistent mechanism of neo-TAD formation in X-LAG. We then identified several pituitary active cis-regulatory elements (CREs) within the neo-TAD and demonstrated in vitro that one of them significantly enhanced reporter gene expression. At the same time, we showed that the GPR101 promoter permits the incorporation of new regulatory information. Our results indicate that X-LAG is a TADopathy of the endocrine system in which Xq26.3 duplications disrupt the local chromatin architecture forming a neo-TAD. Rewiring GPR101-enhancer interaction within the new regulatory unit is likely to cause the high levels of aberrant expression of GPR101 in pituitary tumors caused by X-LAG.
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Kumar A, Sinha S, Jameel J, Khan R, Qureshi OA, Majeed A, Chauhan S, Kumar S. Conventional fluoroscopic views are inadequate to predict the Tip Apex Distance and articular clearance of sliding screw devices: A computed tomography-based analysis. Injury 2022; 53:569-575. [PMID: 34602243 DOI: 10.1016/j.injury.2021.09.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 08/05/2021] [Accepted: 09/17/2021] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Tip-apex-distance (TAD) has been widely advocated as the index to predict the risk of screw cut out in hip fractures treated with sliding hip screw devices. The fluoroscopic extents of the femoral head can change with the slightest change in the limb position which includes internal and external rotations, adduction and abduction. These changes can affect the visible TAD and articular-clearance of the screw-tip. The purpose of this Computed-tomography(CT) based analysis is to analyze the variations of the radiographically visible articular-clearance and TAD measurements with limb positioning and to determine the appropriate fluoroscopic projections for different screw-positions within the femoral head. MATERIAL AND METHODS We retrospectively analysed CT studies of twenty healthy proximal femora. Spatial markers simulating screw tips were placed in the different combinations of anteroposterior(AP) and cephalocaudal(CC) positions. Software-based AP and lateral radiographs were developed for each screw position. Additional AP radiographs with femur in internal and external rotation, and lateral radiographs with the femur in adduction and abduction were developed. The variation of TAD and articular-clearance of the screw was measured among these radiographs for individual screw tip positions. RESULTS Screw tip placed centrally in AP and CC planes position didn't show any significant variation in TAD and articular-clearance with modified AP and lateral radiographs. Significant differences were observed in TAD and articular-clearance values for other screw tip positions. Anteriorly placed screw tips had higher TAD and articular-clearance values with external rotation and similar changes were observed with posteriorly placed tips in internal rotation. Inferiorly placed tips had higher articular-clearance and TAD with limb abduction and similar changes were observed for superiorly placed tips with limb adduction. CONCLUSIONS For the sliding screws placed in non-central locations, the clearance of the screw tip from the articular margins can not be appropriately estimated with conventional AP and lateral views. Additional views with the limb in internal rotation and external rotation in AP view, and adduction-abduction in lateral view are required to safely place the sliding screw in the femoral head. The limb should be brought to a neutral alignment for the accurate estimation of TAD.
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Affiliation(s)
- Arvind Kumar
- Department of Orthopaedics, Hamdard Institute of Medical Sciences and Research, New Delhi, IN, India.
| | - Siddhartha Sinha
- Department of Orthopaedics, Hamdard Institute of Medical Sciences and Research, New Delhi, IN, India.
| | - Javed Jameel
- Department of Orthopaedics, Hamdard Institute of Medical Sciences and Research, New Delhi, IN, India.
| | - Rizwan Khan
- Department of Orthopaedics, Hamdard Institute of Medical Sciences and Research, New Delhi, IN, India.
| | - Owais Ahmed Qureshi
- Department of Orthopaedics, Hamdard Institute of Medical Sciences and Research, New Delhi, IN, India.
| | - Abdul Majeed
- Department of Orthopaedics, Hamdard Institute of Medical Sciences and Research, New Delhi, IN, India.
| | - Shishir Chauhan
- Interventional Radiology, D.Y. Patil Medical College and Research Centre, Pune, Maharashtra, India.
| | - Sandeep Kumar
- Department of Orthopaedics, Hamdard Institute of Medical Sciences and Research, New Delhi, IN, India.
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Maurya RK, Bhardwaj P, Singh H, Mishra HA. Comparative evaluation of duration of extraction space closure and degree of root resorption with conventional and self-Ligation brackets. Indian J Dent Res 2022; 33:52-57. [PMID: 35946245 DOI: 10.4103/ijdr.ijdr_1127_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Introduction Determination of difference between conventional and passive self-ligating brackets (SLBs) in respect of extraction space closure, patient perception and root resorption. Material and Methods Eighty patients were divided into four groups of 20 each with age-sex-matched control using a simple randomisation technique and allocation concealment with a closed opaque envelope method. Group 1 consisted of conventional brackets with Connecticut New Archwire (CNA) wire mushroom loop, group 2 consisted of conventional brackets with TAD (AbsoAnchor, Korea) supported retraction, group 3 consisted of passive SLB with CNA archwires (Libral Traders, India) mushroom loop and group 4 consisted of passive SLB brackets with TAD (AbsoAnchor, Korea) supported retraction. The rate of retraction, root resorption and patient satisfaction were assessed. All conventional brackets (Orthox, USA) and passive SLBs (CaptainOrtho, India) had 0.018 Roth prescriptions with a slot size of 0.018 × 0.025. Results Retraction was the fastest in group 2 with a mean of 1.266 ± 0.14 mm/4 week and a duration of 23.40 weeks. Similarly, group 4 showed the most sluggish movement with a mean of 1.182 ± 0.80 mm/4 weeks with a total duration of 25 weeks; howeverdifferencesce among groups were not statistically significant (P = 0.470). Conclusion SLBs have advantage of better patient comfort, less pain and reduced chairside time. Though the present study found increased treatment duration with SLB along with friction mechanics, refuting the previous claims of reduced friction with SLBs, however, the difference was not statistically significant and results have to be extrapolated with caution and experience considering other advantages of SLBs.
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Affiliation(s)
- Raj Kumar Maurya
- Dental Officer, Department of Orthodontics and Dentofacial Orthopedics, Government Dental Center, Nagaland, India
| | - Preeti Bhardwaj
- Department of Orthodontics and Dentofacial Orthopedics, Mansarovar Dental College, Bhopal, India
| | - Harpreet Singh
- Department of Orthodontics and Dentofacial Orthopedics, ESIC Dental College and Hospital, Rohini, New Delhi, India
| | - Harsh Ashok Mishra
- Department of Orthodontics and Dentofacial Orthopedics, Bharati Vidyapeeth (Deemed to be University) Dental College and Hospital, Navi Mumbai, Maharashtra, India
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Abstract
3D genome mapping aims at connecting the physics of chromatin folding to the underlying biological events, and applications of various chromosomal conformation capture (3C) assays continue to discover critical roles of genome folding in regulating nuclear functions. To interrogate the full spectrum of chromatin folding ranging from the level of nucleosomes to full chromosomes in mammals, we developed an enhanced 3C-based method called Micro-C. The protocol employs Micrococcal nuclease (MNase) to fragment the genome, which overcomes the resolution limit of restriction enzyme-based methods, enabling the estimation of contact frequencies between proximal nucleosomes. Such improvements successfully resolve the fine-scale level of chromatin folding, including enhancer-promoter or promoter-promoter interactions, genic and nucleosomal folding, and boost the signal-to-noise ratio in detecting loops and substructures underlying TADs. In this chapter, we will thoroughly discuss the details of the Micro-C protocol and critical parameters to consider for generating high-quality Micro-C maps.
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Affiliation(s)
- Elena Slobodyanyuk
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Tsung-Han S Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA, USA.
- CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Center for Computational Biology, University of California, Berkeley, Berkeley, CA, USA.
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Tian W, Wang Z, Wang D, Zhi Y, Dong J, Jiang R, Han R, Li Z, Kang X, Li H, Liu X. Chromatin Interaction Responds to Breast Muscle Development and Intramuscular Fat Deposition Between Chinese Indigenous Chicken and Fast-Growing Broiler. Front Cell Dev Biol 2021; 9:782268. [PMID: 34912810 PMCID: PMC8667342 DOI: 10.3389/fcell.2021.782268] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022] Open
Abstract
Skeletal muscle development and intramuscular fat (IMF) content, which positively contribute to meat production and quality, are regulated by precisely orchestrated processes. However, changes in three-dimensional chromatin structure and interaction, a newly emerged mediator of gene expression, during the skeletal muscle development and IMF deposition have remained unclear. In the present study, we analyzed the differences in muscle development and IMF content between one-day-old commercial Arbor Acres broiler (AA) and Chinese indigenous Lushi blue-shelled-egg chicken (LS) and performed Hi-C analysis on their breast muscles. Our results indicated that significantly higher IMF content, however remarkably lower muscle fiber diameter was detected in breast muscle of LS chicken compared to that of AA broiler. The chromatin intra-interaction was prior to inter-interaction in both AA and LS chicken, and chromatin inter-interaction was heavily focused on the small and gene-rich chromosomes. For genomic compartmentalization, no significant difference in the number of B type compartments was found, but AA had more A type compartments versus LS. The A/B compartment switching of AA versus LS showed more A to B switching than B to A switching. There were no significant differences in the average sizes and distributions of topologically associating domains (TAD). Additionally, approximately 50% of TAD boundaries were overlapping. The reforming and disappearing events of TAD boundaries were identified between AA and LS chicken breast muscles. Among these, the HMGCR gene was located in the TAD-boundary regions in AA broilers, but in TAD-interior regions in LS chickens, and the IGF2BP3 gene was located in the AA-unique TAD boundaries. Both HMGCR and IGF2BP3 genes exhibited increased mRNA expression in one-day-old AA broiler breast muscles. It was demonstrated that the IGF2BP3 and HMGCR genes regulated by TAD boundary sliding were potential biomarkers for chicken breast muscle development and IMF deposition. Our data not only provide a valuable understanding of higher-order chromatin dynamics during muscle development and lipid accumulation but also reveal new insights into the regulatory mechanisms of muscle development and IMF deposition in chicken.
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Affiliation(s)
- Weihua Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Zhang Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Dandan Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Yihao Zhi
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Jiajia Dong
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China.,Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou, China.,International Joint Research Laboratory for Poultry Breeding of Henan, Zhengzhou, China
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Katyal S, Yadav V. Diagnostic and Treatment Approach in the Management of Dental Anomalies Associated with Stevens-Johnson Syndrome: A Case Report. Int J Clin Pediatr Dent 2021; 14:569-574. [PMID: 34824516 PMCID: PMC8585912 DOI: 10.5005/jp-journals-10005-1986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Stevens–Johnson syndrome is a rare medical condition with severe mucocutaneous lesions due to adverse drug reactions characterized by exudative multiform erythema, stomatitis, and conjunctivitis. Long-term oral consequences of such cases include xerostomia, caries, impactions, and multiple dental developmental aberrations as short root anomalies. Aim and objective To highlight the role of pedodontist in early diagnosis and treatment planning of dental abnormalities due to Stevens–Johnson syndrome (SJS) using a cone-beam computed tomography (CBCT). Case description A 16-year-old male reported a chief complaint of decayed posterior teeth. Past medical history revealed adverse reactions to an unknown drug at the age of 4 to 5 years. In addition to carious teeth, clinical examination revealed that all canines were missing along with mandibular incisors. On CBCT examination, abnormal short, plump roots with normal crown were seen in all permanent first molars and incisors along with impacted canines and mandibular incisors. This condition was diagnosed as a “Short root anomaly” (SRA) due to SJS. He was found positive to allergy tests for NSAIDs such as ibuprofen and paracetamol. Conclusion NSAIDs can cause a severe adverse reaction resulting in SJS. If this hypersensitivity reaction occurs early during the development of a permanent tooth it may cause dental anomalies such as short roots, root dysmorphia, agenesis, and multiple impacted teeth. Clinical significance This report highlights a unique case of multiple dental aberrations due to SJS and the role of a pedodontist in the early diagnosis and treatment planning of such cases with the help of CBCT. Short root anomalies can be misdiagnosed as root resorption or immature apex. Medical history, clinical and CBCT findings are essential for diagnosis and treatment in SJS patients. Careful orthodontic treatment planning is required in cases of short root anomalies. How to cite this article Katyal S, Yadav V. Diagnostic and Treatment Approach in the Management of Dental Anomalies Associated with Stevens–Johnson Syndrome: A Case Report. Int J Clin Pediatr Dent 2021;14(4):569–574.
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Affiliation(s)
- Sakshi Katyal
- Division of Orthodontics and Dentofacial Deformities, Centre for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
| | - Vijay Yadav
- Division of Conservative Dentistry and Endodontics, Center for Dental Education and Research, All India Institute of Medical Sciences, New Delhi, India
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Guo D, Xie Q, Jiang S, Xie T, Li Y, Huang X, Li F, Wang T, Sun J, Wang A, Zhang Z, Li H, Bo X, Chen H, Liang Z. Synergistic alterations in the multilevel chromatin structure anchor dysregulated genes in small cell lung cancer. Comput Struct Biotechnol J 2021; 19:5946-5959. [PMID: 34849199 PMCID: PMC8604672 DOI: 10.1016/j.csbj.2021.11.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/02/2021] [Accepted: 11/02/2021] [Indexed: 01/01/2023] Open
Abstract
Small cell lung cancer (SCLC) is an aggressive form of lung cancer that uniquely changes the chromosomal structure, although the basis of aberrant gene expression in SCLC remains largely unclear. Topologically associated domains (TADs) are structural and functional units of the human genome. Genetic and epigenetic alterations in the cancer genome can lead to the disruption of TAD boundaries and may cause gene dysregulation. To understand the potential regulatory role of this process in SCLC, we developed the TAD boundary alteration-related gene identification in tumors (TARGET) computational framework, which enables the systematic identification of candidate dysregulated genes associated with altered TAD boundaries. Using TARGET to compare gene expression profiles between SCLC and normal human lung fibroblast cell lines, we identified >100 genes in this category, of which 24 were further verified in samples from patients with SCLC using NanoString. The analysis revealed synergistic chromatin structure alteration at the A/B compartment and TAD boundary levels that underlies aberrant gene expression in SCLC. TARGET is a novel and powerful tool that can be used to explore the relationship of chromatin structure alteration to gene dysregulation related to SCLC tumorigenesis, progression, and prognosis.
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Affiliation(s)
- Dan Guo
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Qiu Xie
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Shuai Jiang
- State Key Laboratory of Proteomics, Institute of Basic Medical Sciences, National Center of Biomedical Analysis, Beijing 100850, China
| | - Ting Xie
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yaru Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xin Huang
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Fangyuan Li
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Tingting Wang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jian Sun
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Anqi Wang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zixin Zhang
- Medical Science Research Centre, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Hao Li
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Xiaochen Bo
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Hebing Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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Abstract
Sex determination is the process by which an initial bipotential gonad adopts either a testicular or ovarian cell fate. The inability to properly complete this process leads to a group of developmental disorders classified as disorders of sex development (DSD). To date, dozens of genes were shown to play roles in mammalian sex determination, and mutations in these genes can cause DSD in humans or gonadal sex reversal/dysfunction in mice. However, exome sequencing currently provides genetic diagnosis for only less than half of DSD patients. This points towards a major role for the non-coding genome during sex determination. In this review, we highlight recent advances in our understanding of non-coding, cis-acting gene regulatory elements and discuss how they may control transcriptional programmes that underpin sex determination in the context of the 3-dimensional folding of chromatin. As a paradigm, we focus on the Sox9 gene, a prominent pro-male factor and one of the most extensively studied genes in gonadal cell fate determination.
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Affiliation(s)
- Meshi Ridnik
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Stefan Schoenfelder
- Epigenetics Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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Drouinaud A, Alain A, Caudron S, Cunique T, Auditeau E, Marcheix PS. Trochanteric fractures treated by internal fixation using short intramedullary nails: Does the visual intraoperative estimation of the Tip-Apex Distance ( TAD) concur with its digital postoperative measurement? Orthop Traumatol Surg Res 2021; 107:103001. [PMID: 34216841 DOI: 10.1016/j.otsr.2021.103001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 01/08/2021] [Accepted: 02/01/2021] [Indexed: 02/03/2023]
Abstract
INTRODUCTION The tip-apex distance (TAD) is the only predictor for mechanical failure after internal fixation of trochanteric fractures. The main objective of our study was to assess whether the intraoperative visual estimation of the TAD concurred with the measurement taken on postoperative digital X-rays. We hypothesized that there was a good concordance between these 2 different methods of measurement. MATERIALS AND METHODS Patients with an isolated trochanteric fracture were included in our study. A hardcopy of the intraoperative X-rays were printed, and the TAD was calculated manually. Radiological and clinical follow-ups were scheduled at 6 weeks, 3 months and 6 months during which numerical measurements of the TAD were taken. We also recorded the fracture type (AO/OTA classification), degree of osteoporosis (Singh index), surgeon experience, age and ASA score. RESULTS A total of 98 patients were included in our study. Of these, 70 had a 6-month follow-up and interpretable postoperative X-rays. The mean age was 87 years, with 77.14% women and a mean ASA score of 3. The coefficient of concordance between the intra and postoperative TAD was 0.7202 (95% CI=0.4905-0.9499). The secondary displacement rate was 3.28%. The univariate analysis showed no statistically significant association between an intraoperative TAD>25mm and fracture type (p=0.7290), degree of osteoporosis (p=0.5701) and surgeon experience (p=1). DISCUSSION/CONCLUSIONS There was a high degree of concordance between intraoperative visual estimation of the TAD and its measurement on postoperative digital X-rays. The treatment of unstable fractures in osteoporotic bone by junior surgeons was not a risk factor for intraoperative TAD>25mm. It is therefore important to educate young surgeons on the concept of TAD and its intraoperative visual estimation technique as it ensures that the cephalic screw is positioned properly during the fixation of trochanteric fractures. LEVEL OF EVIDENCE II.
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Hartmann S, Stachs A, Kühn T, de Boniface J, Banys-Paluchowski M, Reimer T. Targeted Removal of Axillary Lymph Nodes After Carbon Marking in Patients with Breast Cancer Treated with Primary Chemotherapy. Geburtshilfe Frauenheilkd 2021; 81:1121-1127. [PMID: 34629491 PMCID: PMC8494517 DOI: 10.1055/a-1471-4234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/28/2021] [Indexed: 12/24/2022] Open
Abstract
In breast cancer patients who have received primary chemotherapy and then no longer have any suspicious lymph nodes clinically and/or on imaging, marking of initially suspicious axillary lymph nodes with targeted removal has recently been discussed and practised both in Germany and internationally as an alternative to complete axillary lymph node dissection. Tattooing of the suspicious lymph nodes with a highly purified carbon suspension is currently being investigated in clinical studies. Compared with other techniques, the advantages of this method are the high rate of intraoperative lymph node detection, avoidance of an immediately preoperative localisation procedure and the low costs. The practical aspects of lymph node tattooing and the current data regarding this method will be described.
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Affiliation(s)
- Steffi Hartmann
- Universitätsklinikum Rostock, Klinik für Gynäkologie und Geburtshilfe, Rostock, Germany
| | - Angrit Stachs
- Universitätsklinikum Rostock, Klinik für Gynäkologie und Geburtshilfe, Rostock, Germany
| | - Thorsten Kühn
- Klinikum Esslingen, Klinik für Gynäkologie und Geburtshilfe, Esslingen, Germany
| | - Jana de Boniface
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Surgery, Capio St. Göran's Hospital, Stockholm, Sweden
| | - Maggie Banys-Paluchowski
- Universitätsklinikum Schleswig-Holstein, Campus Lübeck, Klinik für Gynäkologie und Geburtshilfe, Lübeck, Germany
- Medizinische Fakultät der Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Toralf Reimer
- Universitätsklinikum Rostock, Klinik für Gynäkologie und Geburtshilfe, Rostock, Germany
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Abstract
Chromatin domains and loops are important elements of chromatin structure and dynamics, but much remains to be learned about their exact biological role and nature. Topological associated domains and functional loops are key to gene expression and hold the answer to many questions regarding developmental decisions and diseases. Here, we discuss new findings, which have linked chromatin conformation with development, differentiation and diseases and hypothesized on various models while integrating all recent findings on how chromatin architecture affects gene expression during development, evolution and disease.
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Affiliation(s)
- Ilias Boltsis
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
| | - Guillaume Giraud
- Department of Cell Biology, Erasmus Medical Centre, Rotterdam, Netherlands
- Cancer Research Center of Lyon – INSERM U1052, Lyon, France
| | - Petros Kolovos
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupolis, Greece
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Chen B, Ma Y, Bi J, Wang W, He A, Su G, Zhao Z, Shi J, Zhang L. Regulation Network of Colorectal-Cancer-Specific Enhancers in the Progression of Colorectal Cancer. Int J Mol Sci 2021; 22:ijms22158337. [PMID: 34361106 PMCID: PMC8348541 DOI: 10.3390/ijms22158337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/31/2021] [Accepted: 08/01/2021] [Indexed: 11/16/2022] Open
Abstract
Enhancers regulate multiple genes via higher-order chromatin structures, and they further affect cancer progression. Epigenetic changes in cancer cells activate several cancer-specific enhancers that are silenced in normal cells. These cancer-specific enhancers are potential therapeutic targets of cancer. However, the functions and regulation networks of colorectal-cancer-specific enhancers are still unknown. In this study, we profile colorectal-cancer-specific enhancers and reveal their regulation network through the analysis of HiChIP data that were derived from a colorectal cancer cell line and Hi-C and RNA-seq data that were derived from tissue samples by in silico analysis and in vitro experiments. Enhancer-promoter loops in colorectal cancer cells containing colorectal-cancer-specific enhancers are involved in more than 50% of the topological associated domains (TADs) changed in colorectal cancer cells compared to normal colon cells. In addition, colorectal-cancer-specific enhancers interact with 152 genes that are significantly and highly expressed in colorectal cancer cells. These colorectal-cancer-specific enhancer target genes include ITGB4, RECQL4, MSLN, and GDF15. We propose that the regulation network of colorectal-cancer-specific enhancers plays an important role in the progression of colorectal cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lei Zhang
- Correspondence: ; Tel./Fax: +86-(22)-23503617
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37
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Abstract
Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matrix factorization, deTOKI seeks regions that insulate the genome into blocks with minimal chance of clustering. deTOKI outperforms competing tools and reliably identifies TAD-like domains in single cells. Finally, we find that TAD-like domains are not only prevalent, but also subject to tight regulation in single cells.
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Affiliation(s)
- Xiao Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China
- School of Life Science, University of Chinese Academy of Sciences, Beijing, People's Republic of China
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Guangjie Zeng
- State Key Laboratory of Software Development Environment, School of Computer Science, Beihang University, 100083, Beijing, People's Republic of China
| | - Angsheng Li
- State Key Laboratory of Software Development Environment, School of Computer Science, Beihang University, 100083, Beijing, People's Republic of China
| | - Zhihua Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China.
- School of Life Science, University of Chinese Academy of Sciences, Beijing, People's Republic of China.
- School of Artificial Intelligence, University of Chinese Academy of Sciences, Beijing, People's Republic of China.
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38
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Kang J, Kim YW, Park S, Kang Y, Kim A. Multiple CTCF sites cooperate with each other to maintain a TAD for enhancer-promoter interaction in the β-globin locus. FASEB J 2021; 35:e21768. [PMID: 34245617 DOI: 10.1096/fj.202100105rr] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/11/2021] [Accepted: 06/15/2021] [Indexed: 01/01/2023]
Abstract
Insulators are cis-regulatory elements that block enhancer activity and prevent heterochromatin spreading. The binding of CCCTC-binding factor (CTCF) protein is essential for insulators to play the roles in a chromatin context. The β-globin locus, consisting of multiple genes and enhancers, is flanked by two insulators 3'HS1 and HS5. However, it has been reported that the absence of these insulators did not affect the β-globin transcription. To explain the unexpected finding, we have deleted a CTCF motif at 3'HS1 or HS5 in the human β-globin locus and analyzed chromatin interactions around the locus. It was found that a topologically associating domain (TAD) containing the β-globin locus is maintained by neighboring CTCF sites in the CTCF motif-deleted loci. The additional deletions of neighboring CTCF motifs disrupted the β-globin TAD, resulting in decrease of the β-globin transcription. Chromatin interactions of the β-globin enhancers with gene promoter were weakened in the multiple CTCF motifs-deleted loci, even though the enhancers have still active chromatin features such as histone H3K27ac and histone H3 depletion. Genome-wide analysis using public CTCF ChIA-PET and ChIP-seq data showed that chromatin domains possessing multiple CTCF binding sites tend to contain super-enhancers like the β-globin enhancers. Taken together, our results show that multiple CTCF sites surrounding the β-globin locus cooperate with each other to maintain a TAD. The β-globin TAD appears to provide a compact spatial environment that enables enhancers to interact with promoter.
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Affiliation(s)
- Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Seongwon Park
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Yujin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
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Long Y, Liu Z, Wang P, Yang H, Wang Y, Zhang S, Zhang X, Wang M. Disruption of topologically associating domains by structural variations in tetraploid cottons. Genomics 2021; 113:3405-3414. [PMID: 34311045 DOI: 10.1016/j.ygeno.2021.07.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/12/2021] [Accepted: 07/21/2021] [Indexed: 01/18/2023]
Abstract
Structural variations (SVs) are recognized to have an important role in transcriptional regulation, especially in the light of resolved 3D genome structure using high-throughput chromosome conformation capture (Hi-C) technology in mammals. However, the effect of SVs on 3D genome organization in plants remains rarely understood. In this study, we identified 295,496 SVs and 5251 topologically associating domains (TADs) in two diploid and two tetraploid cottons. We observed that approximately 16% of SVs occurred in TAD boundary regions that were called boundary affecting-structural variations (BA-SVs), and had a large effect on disrupting TAD organization. Nevertheless, SVs preferred occurring in TAD interior instead of TAD boundary, probably associated with the relaxed evolutionary selection pressure. We noticed the biased evolution of the At and Dt subgenomes of tetraploid cottons, in terms of SV-mediated disruption of 3D genome structure relative to diploids. In addition, we provide evidence showing that both SVs and TAD disruption could lead to expression difference of orthologous genes. This study advances our understanding of the effect of SVs on 3D genome organization and gene expression regulation in plants.
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Affiliation(s)
- Yuexuan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Zhenping Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Hang Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Yuejin Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Sainan Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Maojun Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
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40
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Kim J, Kang J, Kim YW, Kim A. The human β-globin enhancer LCR HS2 plays a role in forming a TAD by activating chromatin structure at neighboring CTCF sites. FASEB J 2021; 35:e21669. [PMID: 34033138 DOI: 10.1096/fj.202002337r] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 04/14/2021] [Accepted: 04/30/2021] [Indexed: 12/31/2022]
Abstract
The human β-globin locus control region (LCR) hypersensitive site 2 (HS2) is one of enhancers for transcription of the β-like globin genes in erythroid cells. Our previous study showed that the LCR HS2 has active chromatin structure before transcriptional induction of the β-globin gene, while another enhancer LCR HS3 is activated by the induction. To compare functional difference between them, we deleted each HS (ΔHS2 and ΔHS3) from the human β-globin locus in hybrid MEL/ch11 cells. Deletion of either HS2 or HS3 dramatically diminished the β-globin transcription and disrupted locus-wide histone H3K27ac and chromatin interaction between LCR HSs and gene. Surprisingly, ΔHS2 weakened interactions between CTCF sites forming the β-globin topologically associating domain (TAD), while ΔHS3 did not. CTCF occupancy and chromatin accessibility were reduced at the CTCF sites in the ΔHS2 locus. To further characterize the HS2, we deleted the maf-recognition elements for erythroid activator NF-E2 at HS2. This deletion decreased the β-globin transcription and enhancer-promoter interaction, but did not affect interactions between CTCF sites for the TAD. In light of these results, we propose that the HS2 has a role in forming a β-globin TAD by activating neighboring CTCF sites and this role is beyond typical enhancer activity.
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Affiliation(s)
- Jiwook Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Jin Kang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - Yea Woon Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
| | - AeRi Kim
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea
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41
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Abstract
Animal genomes are organized into topologically associated domains (TADs). TADs are thought to contribute to gene regulation by facilitating enhancer-promoter (E-P) contacts within a TAD and preventing these contacts across TAD borders. However, the absolute difference in contact frequency across TAD boundaries is usually less than 2-fold, even though disruptions of TAD borders can change gene expression by 10-fold. Existing models fail to explain this hypersensitive response. Here, we propose a futile cycle model of enhancer-mediated regulation that can exhibit hypersensitivity through bistability and hysteresis. Consistent with recent experiments, this regulation does not exhibit strong correlation between E-P contact and promoter activity, even though regulation occurs through contact. Through mathematical analysis and stochastic simulation, we show that this system can create an illusion of E-P biochemical specificity and explain the importance of weak TAD boundaries. It also offers a mechanism to reconcile apparently contradictory results from recent global TAD disruption with local TAD boundary deletion experiments. Together, these analyses advance our understanding of cis-regulatory contacts in controlling gene expression and suggest new experimental directions.
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Affiliation(s)
| | - Antonina Hafner
- Department of Developmental Biology, Stanford UniversityStanfordUnited States
| | - Alistair N Boettiger
- Program in Biophysics, Stanford UniversityStanfordUnited States
- Department of Developmental Biology, Stanford UniversityStanfordUnited States
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42
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Yuan R, Zhang J, Wang Y, Zhu X, Hu S, Zeng J, Liang F, Tang Q, Chen Y, Chen L, Zhu W, Li M, Mo D. Reorganization of chromatin architecture during prenatal development of porcine skeletal muscle. DNA Res 2021; 28:6261936. [PMID: 34009337 PMCID: PMC8154859 DOI: 10.1093/dnares/dsab003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Myofibres (primary and secondary myofibre) are the basic structure of muscle and the determinant of muscle mass. To explore the skeletal muscle developmental processes from primary myofibres to secondary myofibres in pigs, we conducted an integrative three-dimensional structure of genome and transcriptomic characterization of longissimus dorsi muscle of pig from primary myofibre formation stage [embryonic Day 35 (E35)] to secondary myofibre formation stage (E80). In the hierarchical genomic structure, we found that 11.43% of genome switched compartment A/B status, 14.53% of topologically associating domains are changed intradomain interactions (D-scores) and 2,730 genes with differential promoter–enhancer interactions and (or) enhancer activity from E35 to E80. The alterations of genome architecture were found to correlate with expression of genes that play significant roles in neuromuscular junction, embryonic morphogenesis, skeletal muscle development or metabolism, typically, NEFL, MuSK, SLN, Mef2D and GCK. Significantly, Sox6 and MATN2 play important roles in the process of primary to secondary myofibres formation and increase the regulatory potential score and genes expression in it. In brief, we reveal the genomic reorganization from E35 to E80 and construct genome-wide high-resolution interaction maps that provide a resource for studying long-range control of gene expression from E35 to E80.
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Affiliation(s)
- Renqiang Yuan
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xingxing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Silu Hu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Jianhua Zeng
- Guangdong YIHAO Food Co., Ltd, Guangzhou 510620, China
| | - Feng Liang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Yaosheng Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Luxi Chen
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.,Guangdong Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Wei Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Delin Mo
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
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43
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Yasuhara T, Zou L. Impacts of chromatin dynamics and compartmentalization on DNA repair. DNA Repair (Amst) 2021; 105:103162. [PMID: 34182258 DOI: 10.1016/j.dnarep.2021.103162] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/10/2021] [Accepted: 06/17/2021] [Indexed: 11/22/2022]
Abstract
The proper spatial organization of DNA, RNA, and proteins is critical for a variety of cellular processes. The genome is organized into numerous functional units, such as topologically associating domains (TADs), the formation of which is regulated by both proteins and RNA. In addition, a group of chromatin-bound proteins with the ability to undergo liquid-liquid phase separation (LLPS) can affect the spatial organization and compartmentalization of chromatin, RNA, and proteins by forming condensates, conferring unique properties to specific chromosomal regions. Although the regulation of DNA repair by histone modifications and chromatin accessibility is well established, the impacts of higher-order chromatin and protein organization on the DNA damage response (DDR) have not been appreciated until recently. In this review, we will focus on the movement of chromatin during the DDR, the compartmentalization of DDR proteins via LLPS, and the roles of membraneless nuclear bodies and transcription in DNA repair. With this backdrop, we will discuss the importance of the spatial organization of chromatin and proteins for the maintenance of genome integrity.
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Abstract
BACKGROUND While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. RESULTS We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. CONCLUSIONS NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users' preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE .
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Affiliation(s)
- Gulden Olgun
- Department of Computer Engineering, Bilkent University, Ankara, Turkey.,Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Afshan Nabi
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
| | - Oznur Tastan
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey. .,Cancer Data Science Lab, National Cancer Institute, National Institute of Health, Bethesda, MD, USA.
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45
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Abstract
For decades, biochemical methods for the analysis of genome structure and function provided cell-population-averaged data that allowed general principles and tendencies to be disclosed. Microscopy-based studies, which immanently involve single-cell analysis, did not provide sufficient spatial resolution to investigate the particularly small details of 3D genome folding. Nevertheless, these studies demonstrated that mutual positions of chromosome territories within cell nuclei and individual genomic loci within chromosomal territories can vary significantly in individual cells. The development of new technologies in biochemistry and the advent of super-resolution microscopy in the last decade have made possible the full-scale study of 3D genome organization in individual cells. Maps of the 3D genome build based on C-data and super-resolution microscopy are highly consistent and, therefore, biologically relevant. The internal structures of individual chromosomes, loci, and topologically associating domains (TADs) are resolved as well as cell-cycle dynamics. 3D modeling allows one to investigate the physical mechanisms underlying genome folding. Finally, joint profiling of genome topology and epigenetic features will allow 3D genomics to handle complex cell-to-cell heterogeneity. In this review, we summarize the present state of studies into 3D genome organization in individual cells, analyze the technical problems of single-cell studies, and outline perspectives of 3D genomics.
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Affiliation(s)
- Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; Faculty of Biology, M.V. Lomonosov Moscow State University, 119234 Moscow, Russia.
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46
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Soto CJ, Zhao PA, Klein KN, Gilbert DM, Srivastava A. STATISTICAL COMPARISONS OF CHROMOSOMAL SHAPE POPULATIONS. Proc IEEE Int Symp Biomed Imaging 2021; 2021:788-791. [PMID: 35165532 PMCID: PMC8840943 DOI: 10.1109/isbi48211.2021.9433812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This paper develops statistical tools for testing differences in shapes of chromosomes resulting from certain gene knockouts (KO), specifically RIF1 gene KO (RKO) and the cohesin subunit RAD21 gene KO (CKO). It utilizes a two-sample test for comparing shapes of KO chromosomes with wild type (WT) at two levels: (1) Coarse shape analysis, where one compares shapes of full or large parts of chromosomes, and (2) Fine shape analysis, where chromosomes are first segmented into (TAD-based) pieces and then the corresponding pieces are compared across populations. The shape comparisons - coarse and fine - are based on an elastic shape metric for comparing shapes of 3D curves. The experiments show that the KO populations, RKO and CKO, have statistically significant differences from WT at both coarse and fine levels. Furthermore, this framework highlights local regions where these differences are most prominent.
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Affiliation(s)
- Carlos J Soto
- Department of Statistics, Pennsylvania State University, State College, PA, USA
- Department of Statistics, Florida State University, Tallahassee, FL, USA
| | - Peiyao A Zhao
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Kyle N Klein
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Anuj Srivastava
- Department of Statistics, Florida State University, Tallahassee, FL, USA
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47
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Ren K, Li B, Liu Z, Xia L, Zhai M, Wei X, Duan W, Yu S. GDF11 prevents the formation of thoracic aortic dissection in mice: Promotion of contractile transition of aortic SMCs. J Cell Mol Med 2021; 25:4623-4636. [PMID: 33764670 PMCID: PMC8107100 DOI: 10.1111/jcmm.16312] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 12/23/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Thoracic aortic dissection (TAD) is an aortic disease associated with dysregulated extracellular matrix composition and de‐differentiation of vascular smooth muscle cells (SMCs). Growth Differentiation Factor 11 (GDF11) is a member of transforming growth factor β (TGF‐β) superfamily associated with cardiovascular diseases. The present study attempted to investigate the expression of GDF11 in TAD and its effects on aortic SMC phenotype transition. GDF11 level was found lower in the ascending thoracic aortas of TAD patients than healthy aortas. The mouse model of TAD was established by β‐aminopropionitrile monofumarate (BAPN) combined with angiotensin II (Ang II). The expression of GDF11 was also decreased in thoracic aortic tissues accompanied with increased inflammation, arteriectasis and elastin degradation in TAD mice. Administration of GDF11 mitigated these aortic lesions and improved the survival rate of mice. Exogenous GDF11 and adeno‐associated virus type 2 (AAV‐2)‐mediated GDF11 overexpression increased the expression of contractile proteins including ACTA2, SM22α and myosin heavy chain 11 (MYH11) and decreased synthetic markers including osteopontin and fibronectin 1 (FN1), indicating that GDF11 might inhibit SMC phenotype transition and maintain its contractile state. Moreover, GDF11 inhibited the production of matrix metalloproteinase (MMP)‐2, 3, 9 in aortic SMCs. The canonical TGF‐β (Smad2/3) signalling was enhanced by GDF11, while its inhibition suppressed the inhibitory effects of GDF11 on SMC de‐differentiation and MMP production in vitro. Therefore, we demonstrate that GDF11 may contribute to TAD alleviation via inhibiting inflammation and MMP activity, and promoting the transition of aortic SMCs towards a contractile phenotype, which provides a therapeutic target for TAD.
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Affiliation(s)
- Kai Ren
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Buying Li
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Zhenhua Liu
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Lin Xia
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Mengen Zhai
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xufeng Wei
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Weixun Duan
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Shiqiang Yu
- Department of Cardiovascular Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
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48
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Santana JF, Parida M, Long A, Wankum J, Lilienthal AJ, Nukala KM, Manak JR. The Dm-Myb Oncoprotein Contributes to Insulator Function and Stabilizes Repressive H3K27me3 PcG Domains. Cell Rep 2020; 30:3218-3228.e5. [PMID: 32160531 DOI: 10.1016/j.celrep.2020.02.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 09/30/2019] [Accepted: 02/12/2020] [Indexed: 12/13/2022] Open
Abstract
Drosophila Myb (Dm-Myb) encodes a protein that plays a key role in regulation of mitotic phase genes. Here, we further refine its role in the context of a developing tissue as a potentiator of gene expression required for proper RNA polymerase II (RNA Pol II) function and efficient H3K4 methylation at promoters. In contrast to its role in gene activation, Myb is also required for repression of many genes, although no specific mechanism for this role has been proposed. We now reveal a critical role for Myb in contributing to insulator function, in part by promoting binding of insulator proteins BEAF-32 and CP190 and stabilizing H3K27me3 Polycomb-group (PcG) domains. In the absence of Myb, H3K27me3 is markedly reduced throughout the genome, leading to H3K4me3 spreading and gene derepression. Finally, Myb is enriched at boundaries that demarcate chromatin environments, including chromatin loop anchors. These results reveal functions of Myb that extend beyond transcriptional regulation. Myb has been considered a transcriptional activator of primarily M phase genes. Here, Santana et al. show that Myb also contributes to insulator function, in part by promoting binding of insulator factors, and is required to stabilize repressive domains in the genome.
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49
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Liang Z, Zhang Q, Ji C, Hu G, Zhang P, Wang Y, Yang L, Gu X. Reorganization of the 3D chromatin architecture of rice genomes during heat stress. BMC Biol 2021; 19:53. [PMID: 33740972 PMCID: PMC7977607 DOI: 10.1186/s12915-021-00996-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/26/2021] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The three-dimensional spatial organization of the genome plays important roles in chromatin accessibility and gene expression in multiple biological processes and has been reported to be altered in response to environmental stress. However, the functional changes in spatial genome organization during environmental changes in crop plants are poorly understood. RESULTS Here we perform Hi-C, ATAC-seq, and RNA-seq in two agronomically important rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica), to report a comprehensive profile of nuclear dynamics during heat stress (HS). We show that heat stress affects different levels of chromosome organization, including A/B compartment transition, increase in the size of topologically associated domains, and loss of short-range interactions. The chromatin architectural changes were associated with chromatin accessibility and gene expression changes. Comparative analysis revealed that 93-11 exhibited more dynamic gene expression and chromatin accessibility changes, including HS-related genes, consistent with observed higher HS tolerance in this cultivar. CONCLUSIONS Our data uncovered higher-order chromatin architecture as a new layer in understanding transcriptional regulation in response to heat stress in rice.
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Affiliation(s)
- Zhe Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- Centre for Organismal Studies, Heidelberg University, 69120, Heidelberg, Germany
| | - Qian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Changmian Ji
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Guihua Hu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingxian Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yifan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Liwen Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xiaofeng Gu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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50
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Liu X, Sun Q, Wang Q, Hu C, Chen X, Li H, Czajkowsky DM, Shao Z. Epithelial Cells in 2D and 3D Cultures Exhibit Large Differences in Higher-order Genomic Interactions. Genomics Proteomics Bioinformatics 2021; 20:101-109. [PMID: 33631432 PMCID: PMC9510857 DOI: 10.1016/j.gpb.2020.06.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/09/2020] [Accepted: 08/09/2020] [Indexed: 02/07/2023]
Abstract
Recent studies have characterized the genomic structures of many eukaryotic cells, often focusing on their relation to gene expression. However, these studies have largely investigated cells grown in 2D cultures, although the transcriptomes of 3D-cultured cells are generally closer to their in vivo phenotypes. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in higher-order genomic interactions, notably in compartment identity and strength as well as in topologically associating domain (TAD)–TAD interactions, but only minor differences are found at the TAD level. Our RNA-seq analysis reveals an up-regulated expression of genes involved in physiological hepatocyte functions in the 3D-cultured cells. These genes are associated with a subset of structural changes, suggesting that differences in genomic structure are critically important for transcriptional regulation. However, there are also many structural differences that are not directly associated with changes in gene expression, whose cause remains to be determined. Overall, our results indicate that growth in 3D significantly alters higher-order genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
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Affiliation(s)
- Xin Liu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiu Sun
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qi Wang
- Translational Medical Center for Stem Cell Therapy & Institute for Regenerative Medicine, Shanghai East Hospital, School of Life Science and Technology, Shanghai Key Laboratory of Signaling and Disease Research, Tongji University, Shanghai 200092, China
| | - Chuansheng Hu
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuecheng Chen
- Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hua Li
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Daniel M Czajkowsky
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Zhifeng Shao
- State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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